STRING Network Up-regulated genes:
STRING Network Downregulated Genes:
STRING Enrichment Analysis Piecharts:
Visualisation of Ovarian Cancer Network:
Visualisation of Ovarian Cancer Drivers:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RCy3")
library(RCy3)
cytoscapePing()
cytoscapeVersionInfo ()
#4 My first network
nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
group=c("A","A","B","B"), # categorical strings
score=as.integer(c(20,10,15,5)), # integers
stringsAsFactors=FALSE)
edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
target=c("node 1","node 2","node 3","node 3"),
interaction=c("inhibits","interacts","activates","interacts"), # optional
weight=c(5.1,3.0,5.2,9.9), # numeric
stringsAsFactors=FALSE)
createNetworkFromDataFrames(nodes,edges, title="my first network", collection="DataFrame Example")
setVisualStyle('Marquee')
style.name = "myStyle"
defaults <- list(NODE_SHAPE="diamond",
NODE_SIZE=30,
EDGE_TRANSPARENCY=120,
NODE_LABEL_POSITION="W,E,c,0.00,0.00")
nodeLabels <- mapVisualProperty('node label','id','p')
nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA"))
arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',c("activates","inhibits","interacts"),c("Arrow","T","None"))
edgeWidth <- mapVisualProperty('edge width','weight','p')
createVisualStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth))
setVisualStyle(style.name)
lockNodeDimensions(FALSE, style.name)
#5 Bioconductor graph example
g = new ('graphNEL', edgemode='directed')
g = graph::addNode ('A', g)
g = graph::addNode ('D', g)
g = graph::addNode ('C', g, edges = list('D'))
g = graph::addNode ('B', g, edges = list(c('A','D','C')))
createNetworkFromGraph (g, title='simple network', collection='GraphNEL Example')
df <- data.frame (moleculeType=c('kinase','TF','cytokine','cytokine'),
log2fc=c(1.8,3.0,-1.2,-2.5),
row.names = c('A','B','C','D'), # row.names = node names
stringsAsFactors = FALSE) # important when loading strings!
loadTableData (df)
setNodeShapeDefault ('OCTAGON')
setNodeColorDefault ('#AAFF88')
setNodeSizeDefault (60)
setNodeFontSizeDefault (30)
getNodeShapes () # diamond, ellipse, trapezoid, triangle, etc.
column <- 'moleculeType'
values <- c ('kinase', 'TF','cytokine')
shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE')
setNodeShapeMapping (column, values, shapes)
column <- 'log2fc'
control.points <- c (-3.0, 0.0, 3.0)
colors <- c ('#5588DD', '#FFFFFF', '#DD8855')
setNodeColorMapping (column, control.points, colors)
control.points <- c (-2.0, 0.0, 2.0)
colors <- c ('#2255CC', '#5588DD', '#FFFFFF', '#DD8855','#CC5522')
setNodeColorMapping (column, control.points, colors)
control.points = c (-3.0, 2.0, 3.0)
sizes = c (20, 80, 90)
setNodeSizeMapping (column, control.points, sizes)
selectNodes ('C','name')
getSelectedNodes ()
selectFirstNeighbors ()
saveSession('vignette_session') #.cys
full.path=paste(getwd(),'vignette_image',sep='/')
exportImage(full.path, 'PNG', zoom=200) #.png scaled by 200%
exportImage(full.path, 'PDF') #.pdf
?exportImage
#6 Browse available functions, commands and arguments
help(package=RCy3)
cyrestAPI() # CyREST API
commandsAPI() # Commands API
commandsHelp("help")
commandsHelp("help network")
commandsHelp("help network select")
browseVignettes("RCy3")